Package: chromatographR 0.7.1

chromatographR: Chromatographic Data Analysis Toolset

Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in alsace (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (ptw) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (VPdtw) (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.

Authors:Ethan Bass [aut, cre], Hans W Borchers [ctb, cph]

chromatographR_0.7.1.tar.gz
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chromatographR_0.7.1.tgz(r-4.4-any)chromatographR_0.7.1.tgz(r-4.3-any)
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chromatographR.pdf |chromatographR.html✨
chromatographR/json (API)
NEWS

# Install 'chromatographR' in R:
install.packages('chromatographR', repos = c('https://ethanbass.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ethanbass/chromatographr/issues

Datasets:
  • Sa - Raw goldenrod root chromatograms
  • Sa_pr - Preprocessed goldenrod root chromatograms
  • Sa_warp - Warped goldenrod root chromatograms.
  • pk_tab - Goldenrod peak table

On CRAN:

bioinformaticscheminformaticschromatographygc-fidhplchplc-dadhplc-pdahplv-uvmetabolomicsopen-dataopen-sciencereproducibilityreproducible-research

27 exports 13 stars 2.42 score 63 dependencies 1 dependents 6 scripts 30 downloads

Last updated 26 days agofrom:b24f669d3c. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 22 2024
R-4.5-winNOTEAug 22 2024
R-4.5-linuxNOTEAug 22 2024
R-4.4-winNOTEAug 22 2024
R-4.4-macNOTEAug 22 2024
R-4.3-winOKAug 22 2024
R-4.3-macOKAug 22 2024

Exports:attach_metadataattach_ref_spectracluster_spectracombine_peakscorrect_peakscorrect_rtfilter_peaksfilter_peaktablefind_peaksfit_peaksget_agilent_thresholdget_peaksget_peaktableget_puritymerge_peaksmirror_plotnormalize_dataplot_all_spectraplot_chromsplot_spectrumpreprocessread_chromsreshape_chromsreshape_peaktablescan_chromtrim_peakwrite_peaktable

Dependencies:base64encbitbit64bitopscaToolscellrangerchromConverterclicolorspacecpp11crayondata.tabledplyrdynamicTreeCutfansifarverfastclusterFormulafsgenericsglueherehmsjsonlitelabelinglatticelifecyclemagrittrMatrixminpack.lmmunsellpillarpkgconfigpngprettyunitsprogressptwpurrrR6RaMSrappdirsRColorBrewerRcppRcppArmadilloRcppDERcppTOMLreadxlrematchreticulaterlangrprojrootscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLiteVPdtwwithrxml2

chromatographR: An introduction to HPLC-DAD analysis

Ethan Bass^1^

Rendered fromchromatographR.Rmdusingknitr::rmarkdownon Aug 22 2024.

Last update: 2024-08-22
Started: 2021-10-06

Readme and manuals

Help Manual

Help pageTopics
chromatographRchromatographR-package chromatographR
Attach experimental metadataattach_metadata
Attach reference spectraattach_ref_spectra
Make boxplot from peak table.boxplot.peak_table
Cluster peaks by spectral similarity.cluster_spectra
Combine peakscombine_peaks
Correct peak positions according to a ptw warping modelcorrect_peaks
Correct retention timecorrect_rt
Filter peak listsfilter_peaks
Filter peak tablefilter_peaktable
Find peaks in chromatographic profilefind_peaks
Fit chromatographic peaks to an exponential-gaussian hybrid or gaussian profilefit_peaks
Get peak list.get_peaks
Convert peak list into an ordered peak table.get_peaktable
Merge split peaksmerge_peaks
Make mirror plot from peak table.mirror_plot
Normalize peak table or chromatogramsnormalize_data
Goldenrod peak tablepk_tab
Plot all spectra for chosen peak.plot_all_spectra
Plot traces from list of chromatograms.plot_chroms
Plot spectrum from peak tableplot_spectrum
Plot fitted peak shapes.plot.peak_list
Plot spectrum from peak tableplot.peak_table
Plot PTW alignmentsplot.ptw_list
Preprocess time/wavelength datapreprocess
Reshape chromatograms Reshapes a list of chromatograms from wide to long format.reshape_chroms
Reshapes peak table from wide to long formatreshape_peaktable
Raw goldenrod root chromatogramsSa
Preprocessed goldenrod root chromatogramsSa_pr
Warped goldenrod root chromatograms.Sa_warp
Plot spectra by clicking on the chromatogramscan_chrom
Subset peak table Return subset of 'peak_table' object.subset.peak_table
Export peak tablewrite_peaktable